diff --git a/x-pack/plugin/transform/src/main/java/org/elasticsearch/xpack/transform/checkpoint/DefaultCheckpointProvider.java b/x-pack/plugin/transform/src/main/java/org/elasticsearch/xpack/transform/checkpoint/DefaultCheckpointProvider.java
index e624f2e62706b..87614e8a33337 100644
--- a/x-pack/plugin/transform/src/main/java/org/elasticsearch/xpack/transform/checkpoint/DefaultCheckpointProvider.java
+++ b/x-pack/plugin/transform/src/main/java/org/elasticsearch/xpack/transform/checkpoint/DefaultCheckpointProvider.java
@@ -20,11 +20,11 @@
 import org.elasticsearch.client.Client;
 import org.elasticsearch.common.util.set.Sets;
 import org.elasticsearch.xpack.core.ClientHelper;
-import org.elasticsearch.xpack.core.transform.transforms.TransformIndexerPosition;
 import org.elasticsearch.xpack.core.transform.transforms.TransformCheckpoint;
 import org.elasticsearch.xpack.core.transform.transforms.TransformCheckpointStats;
 import org.elasticsearch.xpack.core.transform.transforms.TransformCheckpointingInfo;
 import org.elasticsearch.xpack.core.transform.transforms.TransformConfig;
+import org.elasticsearch.xpack.core.transform.transforms.TransformIndexerPosition;
 import org.elasticsearch.xpack.core.transform.transforms.TransformProgress;
 import org.elasticsearch.xpack.transform.notifications.TransformAuditor;
 import org.elasticsearch.xpack.transform.persistence.TransformConfigManager;
@@ -188,14 +188,12 @@ static Map<String, long[]> extractIndexCheckPoints(ShardStats[] shards, Set<Stri
                 if (checkpointsByIndex.containsKey(indexName)) {
                     // we have already seen this index, just check/add shards
                     TreeMap<Integer, Long> checkpoints = checkpointsByIndex.get(indexName);
-                    if (checkpoints.containsKey(shard.getShardRouting().getId())) {
-                        // there is already a checkpoint entry for this index/shard combination, check if they match
-                        if (checkpoints.get(shard.getShardRouting().getId()) != globalCheckpoint) {
-                            throw new CheckpointException("Global checkpoints mismatch for index [" + indexName + "] between shards of id ["
-                                    + shard.getShardRouting().getId() + "]");
-                        }
-                    } else {
-                        // 1st time we see this shard for this index, add the entry for the shard
+                    // 1st time we see this shard for this index, add the entry for the shard
+                    // or there is already a checkpoint entry for this index/shard combination
+                    // but with a higher global checkpoint. This is by design(not a problem) and
+                    // we take the higher value
+                    if (checkpoints.containsKey(shard.getShardRouting().getId()) == false
+                        || checkpoints.get(shard.getShardRouting().getId()) < globalCheckpoint) {
                         checkpoints.put(shard.getShardRouting().getId(), globalCheckpoint);
                     }
                 } else {
diff --git a/x-pack/plugin/transform/src/test/java/org/elasticsearch/xpack/transform/checkpoint/TransformsCheckpointServiceTests.java b/x-pack/plugin/transform/src/test/java/org/elasticsearch/xpack/transform/checkpoint/TransformsCheckpointServiceTests.java
index d343dd5e0066e..d62a242d8fe16 100644
--- a/x-pack/plugin/transform/src/test/java/org/elasticsearch/xpack/transform/checkpoint/TransformsCheckpointServiceTests.java
+++ b/x-pack/plugin/transform/src/test/java/org/elasticsearch/xpack/transform/checkpoint/TransformsCheckpointServiceTests.java
@@ -43,8 +43,6 @@
 import java.util.Map.Entry;
 import java.util.Set;
 
-import static org.hamcrest.Matchers.containsString;
-
 public class TransformsCheckpointServiceTests extends ESTestCase {
 
     public void testExtractIndexCheckpoints() {
@@ -104,11 +102,15 @@ public void testExtractIndexCheckpointsInconsistentGlobalCheckpoints() {
 
         ShardStats[] shardStatsArray = createRandomShardStats(expectedCheckpoints, indices, randomBoolean(), true, false);
 
-        // fail
-        CheckpointException e = expectThrows(CheckpointException.class,
-                () -> DefaultCheckpointProvider.extractIndexCheckPoints(shardStatsArray, indices));
+        Map<String, long[]> checkpoints = DefaultCheckpointProvider.extractIndexCheckPoints(shardStatsArray, indices);
+
+        assertEquals(expectedCheckpoints.size(), checkpoints.size());
+        assertEquals(expectedCheckpoints.keySet(), checkpoints.keySet());
 
-        assertThat(e.getMessage(), containsString("Global checkpoints mismatch"));
+        // global checkpoints should be max() of all global checkpoints
+        for (Entry<String, long[]> entry : expectedCheckpoints.entrySet()) {
+            assertArrayEquals(entry.getValue(), checkpoints.get(entry.getKey()));
+        }
     }
 
     /**
@@ -176,8 +178,8 @@ private static ShardStats[] createRandomShardStats(Map<String, long[]> expectedC
                 }
 
                 // SeqNoStats asserts that checkpoints are logical
-                long localCheckpoint = randomLongBetween(0L, 100000000L);
-                long globalCheckpoint = randomBoolean() ? localCheckpoint : randomLongBetween(0L, 100000000L);
+                long localCheckpoint = randomLongBetween(100L, 100000000L);
+                long globalCheckpoint = randomBoolean() ? localCheckpoint : randomLongBetween(100L, 100000000L);
                 long maxSeqNo = Math.max(localCheckpoint, globalCheckpoint);
 
                 SeqNoStats validSeqNoStats = null;
@@ -221,7 +223,7 @@ private static ShardStats[] createRandomShardStats(Map<String, long[]> expectedC
                     if (inconsistentReplica == replica) {
                         // overwrite
                         SeqNoStats invalidSeqNoStats =
-                            new SeqNoStats(maxSeqNo, localCheckpoint, globalCheckpoint + randomLongBetween(10L, 100L));
+                            new SeqNoStats(maxSeqNo, localCheckpoint, globalCheckpoint - randomLongBetween(10L, 100L));
                         shardStats.add(
                             new ShardStats(shardRouting,
                                 new ShardPath(false, path, path, shardId), stats, null, invalidSeqNoStats, null));